Darkest Depths
by Alynxide
Summary: Unbeknownst to Sherlock, the scientists at Baskerville got their hands on his DNA. Except they didn't know the havoc that would cause over a hundred years into the future. Now Starfleet needs assistance and Sherlock needs answers. And he and John are sucked into a case they just can't solve. Rating may change. Romance later, too.
1. Bored Milk

"John!" Sherlock's voice boomed from the kitchen. The blonde haired blogger rushed into the kitchen with worry painted on his face. "We are out of milk." John's worried expression faded as it was replaced with one of annoyance and disbelief.

"How many times have I told you Sherlock, go get the bloody milk!" John raised his voice near the end.

"More times than I have actually gotten the milk," Sherlock smirked as John huffed and turned away, heading for his coat. Without a word he left the flat. Sherlock smiled to himself thinking about John always giving into his ridiculous requests. He made his way to his chair, flicking on the television before sitting down. He drew his knees to his chest as the program flickered on the screen. For a moment he felt guilty about making John go out, but then he remembered how much he didn't want to go himself. With an angry huff, he closed his eyes.

Sherlock hadn't had a case in weeks, and it was driving him mad with boredom. He tried to busy himself with experiments but it wasn't enough. He also worried that he had been on John's nerves more than usual. The man seemed so short with him the past few days. But Sherlock didn't give much thought to it, he had bigger problems. Like the fact that he needed a case to stimulate his constant running mind. He ran a hand through his dark curls in frustration. Something had to come up soon.

The damp London streets glistened as light danced across the pavement and the night air was thick with the scent of rain. John pushed his hands farther into his coat pockets and hurried down the sidewalk. He checked his watch, realizing it was already eight twenty three as he neared the store. He silently cursed Sherlock for making him go out this late. Then he realized Sherlock didn't really make him do this, and so he cursed him again for being a manipulative bastard.

The automatic doors slid open and he stepped inside the unusually crowded store. He kept his eyes straight ahead of him as he made his way to the refrigerated section. He wasn't in the mood to chat with anyone, he just wanted to get back to the flat. The cool air chilled his skin as he opened the refrigerator door and took two cartons of milk. His text tone erupted from his pocket as he was walking back to the check out line. He ignored the text, certain it was Sherlock in need of something else ridiculous, like the remote which was probably a few feet out of reach. He approached the counter and placed the milk down. He suddenly realized how incredibly tired he was. His phone went off again but he still didn't bother taking it out of his pocket. Sherlock could get whatever he needed himself. Or he could wait. John didn't really care.

Sherlock sat staring at his phone, eagerly awaiting John's reply. He didn't like this program. It was boring, but the remote was on the desk. It was eight fifty four and Sherlock started to wonder what was taking John so long. His phone suddenly chimed as it received a text, but to his disappointment it was only Mycroft.

Hello dear brother. Something has come up it seems. We need to have a chat. In person. -M

Sherlock started to reply but was interrupted as the door swung open, revealing a very tired looking John who went straight into the kitchen.

"John ca-"

"No," John said as he put the milk away and began to head upstairs. Sherlock sighed and stood up. He didn't even want to watch telly anymore.

"John."

"I'm going to bed Sherlock," John sighed. Sherlock wanted to stop him, but instead he seated himself at the desk and opened his laptop. Once again, his phone chimed with yet another text message and he realized he never replied.

As soon as possible. It is urgent, Sherlock. -M


	2. A Disappointment As Always

Sherlock and John hurried out of the door of 221B and flagged down a cab. They had just gotten a call from Lestrade about two murder victims and Sherlock was ecstatic. This one was a bit strange, or so that's what Lastrade had told them, which made Sherlock all the more excited. A cabbie finally stopped for them and John opened the door, sliding in before Sherlock.

"It's about time something came up," Sherlock said, looking out the window.

"I agree, I was afraid you would end up destroying the flat," John muttered, checking his phone. Sherlock didn't respond and the two continued to ride in silence. John shifted uncomfortably, looking out the window at the rain clouds looming above. He glanced back at Sherlock, who seemed to be in deep thought, which wasn't unusual for dark haired man. John pinched the bridge of his nose and squeezed his eyes shut. He didn't sleep well the night before. Sherlock was up playing the violin all night. John was used to such things by now, but it didn't mean he slept any better.

"Two," Sherlock stated at random.

"Wha?" John snapped out of his thought.

"Lestrade said there were two victims,"

"He did. What are you going on about Sherlock?" John furrowed his brow in confusion.

The cab stopped abruptly as they pulled into their destination which appeared to be an abandoned storage department. Sherlock didn't answer John once again as he exited the cab. John rolled his eyes and followed behind Sherlock. Police cars sat around the crime scene, which was marked off with the usual bright yellow tape. John followed Sherlock to the building, where Lestrade greeted them. The three entered the building, which was dark and smelled like decayed wood.

"They were found this morning, no sign of the killer," Lastrade told them as he lead them to the corpses. "But, here's the weird part," He said motioning towards the bodies. They were laying at the center of an empty room, arms crossed over their chests. Their clothing was neat and appeared untouched. As Sherlock and John approached, he could see there was something carved into their foreheads.

"What's this?" John asked as he took a knee. He observed the cuts. They were precisely carved letters, but were not in any particular order. "They're letters."

"Thank you for that lovely observation, John," Sherlock retorted sarcastically.

"Alright genius detective. I apologize. Work your magic," John snapped. The corners of Sherlock's mouth twitched upwards for a brief moment and he drew in a sharp breath.

"The cuts are clean and precise, which means they were probably made with a scalpel. The letters aren't arranged into any particular words, which could mean that they stand for something. But what…?" Sherlock trailed off as he began searching pockets and the insides of sleeves. His eyes lit up as he pulled a slip of paper out of one man's shoe. "Ah! Yes!" He unfolded the paper and read it aloud. "A notable Roman."

"What could that mean?" John questioned.

"Ceasar," Sherlock announced. "It's coded using the Ceasar cipher. One of the simplest encryption techniques. It's simply a shift of the letters. We're dealing with someone who _thinks_ they're clever."

"Well do you know what it stands for?" Lestrade asked.

"I would have to look at the cipher," Sherlock answered. "John, get a picture of the bodies."

Without hesitation, John pulled out his phone and took a picture of the corpses. He took two more of their foreheads, then healed back down to further inspect the bodies.

"Sherlock, look," John pointed to the back of one man's head and titled it over.

"Blunt force trauma," Sherlock mumbled.

The ride back to the flat was as quiet as the one there. Sherlock was on his phone most of the ride, probably looking at the cipher. At least John assumed so. It was now pouring rain.

"It was just another boring one," Sherlock began.

"It was something," John told him.

"This one will take no time for solve, the poor fool thinks he's smart or mysterious by leaving us some kind of message."

"We don't know if it wil lead us to him," John stated.

"He's an idiot. Of course it will."

John laughed. "Well I think we should stop for lunch before we head back to the flat."

"Chinese?" Sherlock smiled.

"Definitely," John replied before asking the cabbie to take them to their new destination.

The detective and his blogger sat at a small table near the back of the resturant. John's blonde hair was tousled and he had a plateful of food, while Sherlock had nothing but water. The two discussed various things, possiblilites for the case, and Sherlock's violin playing the previous night. The dective and his blogger hadn't gone out together in quite sometime. Sherlock figured it was because John hated it when people assumed they were a couple. Sherlock on the other hand didn't care what people thought. He knew they weren't a couple and he thought that was all that mattered. He didn't really understand why John worried so much about such things. Maybe it was the women, or sometihng. He never took too much interest in the women John brought around, because he knew they wouldn't be there long. He wasn't saying there was anything wrong with John, because as far as he could see there wasn't. He seemed to care about and do what he could for his girlfriends, but somehow, things always failed. John had never really bothered to talk about it to Sherlock. He probably thought Sherlock wouldn't understand.

Sherlock was snapped out of his thoughts when John got up to refil his plate. He watched the shorter, greying man walk off. He took out his phone and and was about to start looking back over the pictures from the crime scene when he saw he had text from his brother. He didn't feel like reading it so he just put his phone away again. By now John had returned with more food and Sherlock had begun to feel a bit hungry himself. He picked up a fork and jabbed it into a piece of chicken on John's plate.

"What the hell Sherlock?!" John spat.

"Hungry," Sherlock mumbled through a mouthful of chicken.

"We're at a buffet!"

"Couldn't be bothered to get up."

"Well, Sherlock, have this plate, I'll go fix another one," John sighed as he started to get up.

"No don't bother," Sherlock said as he stood and left the restaurant. Once outside he checked his phone again and decided to read the text from Mycroft.

_Your flat in 20 minutes. -M_

Sherlock flagged down another cab and told them where to go. John still sat set the table, confused as he watched Sherlock get into a cab and drive away.


	3. Big Brother Let The Cat Out

Mycroft's footsteps echoed up the stairs as he approached his younger brother's flat. He swallowed hard. He usually had no trouble telling things to people, let alone his little brother. But this wasn't just anything, and he had no idea how Sherlock would react. When he reached the door he let himself in to find Sherlock already seated in his chair. Mycroft approached Sherlock slowly and took the seat next to his. He remained silent, waiting for Sherlock to speak. Sherlock said nothing.

"Do you remember your little visit to Baskerville?" Mycroft asked coldly.

"What of it?" Sherlock questioned.

"We all know they've been doing human experimenting. At the time of your visit they were in the midst of one of the biggest projects they have ever worked on. All they needed was DNA." Mycroft looked at the floor, thinking of the words to complete his next statement. It was clear that he was a bit distressed, Sherlock noticed this right away.

"Go on," Sherlock insisted. He hated when people dragged on explanations to unnecessary lengths. It was both boring and tedious. So far this wasn't catching his interest. But he decided he would hear the entire story before sending Mycroft away with a no.

"This project, titled Project Rodin, was a test of many different things. It would experiment with DNA enhancement, extremely accelerated growth, and cloning." Sherlock looked up at Mycroft and raised an eyebrow. He was somewhat interested now.

"So what exactly are you asking me to do?" Sherlock shifted in his seat. It wasn't a rare occurrence for Mycroft to ask Sherlock for help on a case. Although they were usually on a high scale of importance and Sherlock typically found them very boring.

"Sherlock, this isn't a case," Mycroft sighed. "Essentially this project was aimed at creating a genetically enhanced human. A 'superhuman' if you must. But the idea was to clone it to a prime age so that they wouldn't have to wait twenty or thirty years for it to grow up."

"What are you getting at Mycroft. If this isn't a case then why tell me this?" Sherlock snorted.

"Because it involves you, Sherlock."

"Involves me? What do y-" Sherlock stopped mid sentence as it clicked in his mind. "They.."

At that moment, the door swung open to reveal a very soaked John Watson. He was about to open his mouth to speak, but noticed Mycroft and the very tense mood. He realized this must've been why Sherlock left in a rush. His anger towards the man melted away, especially when he noticed the very disturbed expression on his face.

"Used your DNA, yes," Mycroft finished the statement for him. "They found you impressive. Physically fit and intelligent. Perfect factors for the base traits of superhuman DNA."

"Did it work?" Sherlock demanded, snapping his head back in Mycroft's direction.

"Wait, used Sherlock's DNA? What?" John piped in, clearly confused.

"I never got word back on that," Mycroft stated.

"Anyone going to tell me what's going on?!" John raised his voice a bit. The brothers ignored him and continued talking.

"How long have you known about this?" Sherlock snapped.

"A was informed only days before I first asked to speak with you." Mycroft stood up, walking around his chair and to the window. "This is confidential information. I'm breaking enough rules by just telling you, Sherlock." Mycroft turned to face John and Sherlock as he headed towards the door. "And Sherlock," Mycroft said as he looked back at the two, "don't do anything irrational." And with that he stepped out, the door clicking shut behind him.

Neither John or Sherlock said a word at first. Sherlock's expression was blank and he stared at a fixed point. John was the first to speak.

"Well, uh…" He tried to figure out what to say. He still had no idea what was going on. He wasn't sure he liked what he did hear of that conversation. Sherlock stood abruptly, wordlessly walking past John and grabbing his coat.

"Sherlock, where are you going?" John questioned as Sherlock wrapped his scarf around his neck.

"Out," Sherlock stated, slamming the door behind him. John groaned and sat on the couch. He buried his face in his hands. He hated it when Sherlock got into these moods. It was like the man didn't even consider John's presence or the fact that John cared. John knew he probably didn't. It was something he had learned to deal with during his time with Sherlock. It wasn't unusual for Sherlock to disregard John's concern. John suddenly remembered how soaking wet he was. He got up from the couch and groggily walked up to his room to change into something dry. There was no telling when Sherlock would be back. So he would be up, worrying his ass off about what was going on. It was going to be a long night.


	4. No Big Deal

**I just wanna say thank you all for the nice reviews! It means a lot, even if I don't reply to them 3**

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It was still dark in 221B when John awoke from his slumber. It was nearly 3 in the morning and yet Sherlock was still gone. John sat up and rubbed his sleep filled eyes. He reached over and took his phone from his night stand. No messages. A heavy sigh escaped his lips and he fell back onto the bed. He was worried about Sherlock, but that wasn't unusual. Sherlock was probably fine, but John was concerned about what had put him in this mood and why. He thought about asking Mycroft, but decided he probably wouldn't get the answer he was looking for.

John laid in bed wide awake for nearly an hour before deciding to get up and make himself something to drink. That's was when he saw the file folder sitting on the coffee table where Mycroft had placed it hours before. He picked it up and started observing it.

_Project Rodin. _He opened it, removing the bulk of paper from it and began reading. His mouth went dry and hung open just a bit.

"Oh God."

Meanwhile, Sherlock paced up the dark streets. He had been walking for hours. At first he took a cab to a small dine-in and sat thinking until they kicked him out at closing time. Since then he'd been wandering the streets of London, his mind racing. His thoughts then wandered back to John. He considered how worried the man might be. John didn't even know what was going on. Sherlock figured that he had gone to bed without waiting up. Something Sherlock always failed to understand was why John did such things. He know John cared but he never saw the logic behind such actions. His mind sped back to what Mycroft had told him. He had tried to use his thoughts about John to avoid thinking about it, and yet his mind continued to stray back.

It was late and Sherlock had lost track of time. He pulled out his phone to check and saw that he had a text.

_I read the file. -JW_

He saw the text had only been sent a few minutes before. John was still up. Sherlock wanted John to remain up so sent him a quick reply.

_Home soon. -SH_

John jumped at the sound of his phone going off. He hadn't expected Sherlock to reply, as he often does not. Especially not when he goes out on his "thinking walks". John was sitting in his chair still flipping through the contents of the file. He put his phone back down and continued studying the file. He had no idea how long Sherlock would be, but he didn't mind staying up. He wasn't tired anyways, not now.

He thumbed through the written articles. They explained that they were in need of DNA to initiate the project. But they needed the DNA of someone who was already highly intelligent and physically fit. John rolled his eyes. Sherlock all over. There was an entry about the consideration of Sherlock Holmes as a supplier of the DNA and information about how they planned to manipulate the cloned DNA. There were photos of Sherlock paperclipped to write ups. They were serious about this. It was pretty creepy.

It took Sherlock another twenty minutes to return to the flat.

Sherlock strode in as if it weren't the hour that it was. He looked at John, who was now very tired looking. John stood and took a seat at the desk. Sherlock sat on the couch and steepled his fingers.

"I uh, saw the file," John said, interlocking his fingers and looking at Sherlock.

"Yes..." Sherlock trailed off, sounding uninterested.

"So they wanted to clone the great Sherlock Holmes, huh?"

"Mycroft says I impressed them." The corners of Sherlock's mouth twitched up.

"Says here they uh, "enhanced" the DNA," John said as he filed through the papers.

"Yes, John."

"This is insane. Aren't they supposed to get consent before they use you as a donor for anything?" John's tone suddenly became very serious.

"Do you think they care about 'consent' John?"

"Is this even legal?"

Sherlock didn't reply.

"Is this not a big deal to you Sherlock?!"

No reply.

"Damnit Sherlock! This is not okay!"

"Pack your bags John," Sherlock said calmly.

"What?" John was shocked. Did he make Sherlock that angry?

"We're going to Baskerville."

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**A/N **

**Short chapter is short. I apologize, school this week had me too busy and tired to work on this, plus I didn't have much inspiration for this chapter. But I've had so many asking me to update the last few days I decided to wrap this chapter up.**


	5. Give Me Sleep

**A/N:** I'm so sorry for the delayed update. I rewrote this chapter two times. I'm still not really happy with it but! oh well.

Thank you guys for all the nice feedback on the previous chapter, by the way! Your reviews/favorites/follows mean a lot!

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Darkness still enveloped the London streets when John and Sherlock left the flat. A cab was already waiting for them. John tossed the bags into the floorboard as the two shuffled sleepily inside.

"Dartmoor right?" The cabbie asked, looking back.

"Right," John nodded.

Neither of them said anything for quite sometime after that, until Sherlock decided to break the silence.

"You did call about rooming, right John?"

"I did," John replied.

"Very well," Sherlock said, returning his gaze out of the window.

"And I made sure they had two beds."

Sherlock didn't respond. He checked his phone, then returned it to his pocket.

"So Sherlock. What are you going to do if we actually do find something here?" John questioned curiously.

"I don't know," Sherlock muttered.

"Well what can we do?"

Sherlock ignored John again, as he was deep in thought. John sighed heavily as his minded wandered through the possibilites of what they might discover. What would they do? What _could_ they do? Sherlock's fingers tapped away on his knee while he stared out the window and John shifted in his seat, trying to make himself comforable. The steady hum of the cab in his ears mixed with the lack of voices finally pulled him into much needed sleep.

The rest of ride was long and boring for Sherlock, he never slept on rides, but the two finally arrived at their destination. John took the bags to check in as Sherlock paid the driver. He made his way to the front desk at the inn.

" Can I help you sir?" A young lady with golden hair that was pulled into a neat ponytail asked him.

"Ah yes, I'd like to check in." John smiled.

"Name please?" She smiled as she went over to the computer.

"Watson,"

"Here you are." Her blue eyes flickered in his direction and she handed him a pair of room keys.

"Thank you," He gave a slight nod and took the room keys along with their things. He realized Sherlock wasn't with him, but didn't worry himself over his location. He made his way to their room and unlocked the door. He sat their things aside and closed the door behind him. Something didn't seem right though. He crossed his arms. Then it hit him.

There was only one bed.

Bloody hell. Just great.

Sherlock made his way to the small pub where they had met the innkeepers during their first visit. He hoped to find out if anyone had noticed anymore suspicious or peculiar activity from Baskerville. Of course most everything people heard and said about Baskerville was rumors and hearsay. It was a secret military base after all. Secrets would be kept. Especially something like creating a superhuman clone. As he neared the entrance of the pub, his attention was caught by an odd looking man in a trench coat who sat at a small table sipping coffee behind a newspaper.

"Sherlock!" One of the innkeepers saw him and waved him over to the register. "What are you doing back here?"

"Vacationing," Sherlock lied. His eyes scanned the room, paying little to no attention to the conversation. He managed to walk away and seat himself at a table across from the man he'd noticed when he walked in. His phone chimed from his pocket.

_Where are you? -JW_

Before he could reply, John made his way inside.

"Oh Sherlock I was just-"

"I know." Sherlock wiggled his phone in front of John's face. John rolled his eyes and sat down across from Sherlock.

"That man," Sherlock whispered, motioning his head towards the man in the coat. John looked over his shoulder. "He seems very peculiar. He's obviously nervous about sometihng. He's hurring to finish his coffee and he keeps looking over his newspaper to survey his surroundings. He's not really reading it, just pretending so no one will bother him."

"Okay what are you getting at?" John raised an eyebrow.

"He has his coat buttoned but if you look closely you can see a lab coat underneath. He works for Baskerville."

"Okay. But isn't Mycroft going to allow you access back inside?"

"He is, I was merely observing this man's odd behavior." Sherlock smirked.

"What doe that tell us though?"

"He clearly does not want to be spoken to. He knows something but doesn't want to risk telling it. It's obviously something big." Sherlock speaks quickly and softly.

"Well obviously something isn't right then. You can rent us another vehicle and we'll head to Baskerville first thing tomorrow," John said as he stood up. "I'm going back to the room, I need sleep." John slipped Sherlock his key and retreated back to their room.

Sherlock strode back to the room an hour or so after John left. It was now late evening and the setting sun cast an orange haze across the land. He had just returned from renting their vehicle, the same silver Land Rover that they had previously driven here. He stepped up to the door, unlocking it, he swung it open and stepped inside. John jumped up from his sleep. His greying hair was tousled and he stared drowsily at Sherlock. He had gotten used to rude awakenings and lack of consideration during his time with Sherlock.

"Didn't mean to wake you." Sherlock closed to door behind him, eyeing John as he noticed the missing bed right away.

"Ah.. yeah.. I talked to them, this was the only available room that they could reserve for us. So, I'll just sleep on the floor, or something," John gave a half smile. Sherlock just looked at him and walked away.

John couldn't peel himself off the bed. Sleep beckoned him back into its arms. He needed it so bad. He heard the sound of the shower come on. He could just get up when Sherlock got out. Yeah. That's what he'd do. His heavy lids fluttered closed and the sound of the shower lulled him back into a deep sleep.


	6. Update: Please Read

So guys. I just want to apologize for taking so long to update.

Just letting you all know I haven't forgotten about this story.

Update tes is coming soon.

The past few weeks have been hectic.

Last weekend I was on a youth trip and I've had to do senior stuff for school and AP classes are no.

Last week was eh so inspiration has been running short.

I will be trying to write the next chapter this week. Thanks for understanding guys.


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